Starting phenix.real_space_refine on Wed Jul 23 16:51:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p16_13157/07_2025/7p16_13157.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p16_13157/07_2025/7p16_13157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2025/7p16_13157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2025/7p16_13157.map" model { file = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2025/7p16_13157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p16_13157/07_2025/7p16_13157.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 23 5.16 5 C 2412 2.51 5 N 561 2.21 5 O 624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3621 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2617 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 7, 'TRANS': 310} Chain breaks: 2 Chain: "B" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 964 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 3.43, per 1000 atoms: 0.95 Number of scatterers: 3621 At special positions: 0 Unit cell: (76.818, 102.858, 70.308, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 23 16.00 P 1 15.00 O 624 8.00 N 561 7.00 C 2412 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 102 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 538.9 milliseconds 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 824 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 68.0% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.587A pdb=" N PHE A 8 " --> pdb=" O THR A 4 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N MET A 10 " --> pdb=" O CYS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 36 removed outlier: 4.482A pdb=" N THR A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 67 removed outlier: 3.565A pdb=" N PHE A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.605A pdb=" N PHE A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A 96 " --> pdb=" O TYR A 92 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N HIS A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 141 removed outlier: 3.521A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 156 removed outlier: 4.092A pdb=" N LEU A 149 " --> pdb=" O PRO A 145 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 156 " --> pdb=" O TYR A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 190 removed outlier: 3.723A pdb=" N LEU A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 198 through 227 removed outlier: 4.140A pdb=" N LYS A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 250 removed outlier: 3.576A pdb=" N VAL A 231 " --> pdb=" O ASP A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 247 " --> pdb=" O PHE A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.761A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE A 273 " --> pdb=" O PHE A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 281 removed outlier: 4.394A pdb=" N GLN A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.513A pdb=" N VAL A 293 " --> pdb=" O CYS A 289 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 343 removed outlier: 3.992A pdb=" N ILE A 319 " --> pdb=" O SER A 315 " (cutoff:3.500A) Proline residue: A 320 - end of helix removed outlier: 3.754A pdb=" N VAL A 326 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.518A pdb=" N LYS B 71 " --> pdb=" O ASP B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 97 removed outlier: 3.684A pdb=" N THR B 97 " --> pdb=" O PRO B 94 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N VAL B 18 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B 55 " --> pdb=" O TRP B 42 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG B 44 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY B 53 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.588A pdb=" N VAL B 18 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL B 128 " --> pdb=" O ALA B 98 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA B 98 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N TYR B 101 " --> pdb=" O PHE B 43 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 105 " --> pdb=" O TYR B 38 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.93 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 526 1.31 - 1.44: 1140 1.44 - 1.56: 2016 1.56 - 1.69: 2 1.69 - 1.81: 34 Bond restraints: 3718 Sorted by residual: bond pdb=" C' PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sigma weight residual 1.332 1.425 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" CB PLC A 401 " pdb=" O3 PLC A 401 " ideal model delta sigma weight residual 1.327 1.420 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " ideal model delta sigma weight residual 1.503 1.553 -0.050 2.00e-02 2.50e+03 6.23e+00 bond pdb=" C4 PLC A 401 " pdb=" C5 PLC A 401 " ideal model delta sigma weight residual 1.511 1.558 -0.047 2.00e-02 2.50e+03 5.62e+00 bond pdb=" CB PLC A 401 " pdb=" C1B PLC A 401 " ideal model delta sigma weight residual 1.504 1.551 -0.047 2.00e-02 2.50e+03 5.48e+00 ... (remaining 3713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.21: 5010 3.21 - 6.42: 34 6.42 - 9.64: 5 9.64 - 12.85: 2 12.85 - 16.06: 1 Bond angle restraints: 5052 Sorted by residual: angle pdb=" O3P PLC A 401 " pdb=" P PLC A 401 " pdb=" O4P PLC A 401 " ideal model delta sigma weight residual 93.62 109.68 -16.06 3.00e+00 1.11e-01 2.87e+01 angle pdb=" C5 PLC A 401 " pdb=" N PLC A 401 " pdb=" C7 PLC A 401 " ideal model delta sigma weight residual 106.97 119.04 -12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" N LEU B 114 " pdb=" CA LEU B 114 " pdb=" C LEU B 114 " ideal model delta sigma weight residual 114.56 109.89 4.67 1.27e+00 6.20e-01 1.35e+01 angle pdb=" C ILE A 278 " pdb=" N LYS A 279 " pdb=" CA LYS A 279 " ideal model delta sigma weight residual 121.54 128.39 -6.85 1.91e+00 2.74e-01 1.29e+01 angle pdb=" O1P PLC A 401 " pdb=" P PLC A 401 " pdb=" O2P PLC A 401 " ideal model delta sigma weight residual 119.61 109.03 10.58 3.00e+00 1.11e-01 1.24e+01 ... (remaining 5047 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.46: 2023 30.46 - 60.92: 89 60.92 - 91.38: 10 91.38 - 121.85: 0 121.85 - 152.31: 2 Dihedral angle restraints: 2124 sinusoidal: 827 harmonic: 1297 Sorted by residual: dihedral pdb=" C2' PLC A 401 " pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " pdb=" O2 PLC A 401 " ideal model delta sinusoidal sigma weight residual 169.53 17.22 152.31 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C2' PLC A 401 " pdb=" C' PLC A 401 " pdb=" C1' PLC A 401 " pdb=" O' PLC A 401 " ideal model delta sinusoidal sigma weight residual -11.03 -161.60 150.57 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CA ILE A 16 " pdb=" C ILE A 16 " pdb=" N ILE A 17 " pdb=" CA ILE A 17 " ideal model delta harmonic sigma weight residual 180.00 160.23 19.77 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 385 0.033 - 0.067: 148 0.067 - 0.100: 30 0.100 - 0.133: 8 0.133 - 0.166: 1 Chirality restraints: 572 Sorted by residual: chirality pdb=" C2 PLC A 401 " pdb=" C1 PLC A 401 " pdb=" C3 PLC A 401 " pdb=" O2 PLC A 401 " both_signs ideal model delta sigma weight residual False -2.31 -2.48 0.17 2.00e-01 2.50e+01 6.91e-01 chirality pdb=" CG LEU B 87 " pdb=" CB LEU B 87 " pdb=" CD1 LEU B 87 " pdb=" CD2 LEU B 87 " both_signs ideal model delta sigma weight residual False -2.59 -2.71 0.12 2.00e-01 2.50e+01 3.62e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.28e-01 ... (remaining 569 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 190 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO A 191 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 191 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 191 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 73 " 0.130 9.50e-02 1.11e+02 5.86e-02 2.24e+00 pdb=" NE ARG B 73 " -0.010 2.00e-02 2.50e+03 pdb=" CZ ARG B 73 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 73 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 73 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 123 " 0.006 2.00e-02 2.50e+03 1.29e-02 1.65e+00 pdb=" CD GLU A 123 " -0.022 2.00e-02 2.50e+03 pdb=" OE1 GLU A 123 " 0.008 2.00e-02 2.50e+03 pdb=" OE2 GLU A 123 " 0.008 2.00e-02 2.50e+03 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 100 2.72 - 3.27: 3862 3.27 - 3.81: 5788 3.81 - 4.36: 6594 4.36 - 4.90: 11142 Nonbonded interactions: 27486 Sorted by model distance: nonbonded pdb=" O THR A 139 " pdb=" N GLY A 143 " model vdw 2.178 3.120 nonbonded pdb=" NZ LYS A 209 " pdb=" OG1 THR A 274 " model vdw 2.261 3.120 nonbonded pdb=" OG SER A 132 " pdb=" OD2 ASP A 181 " model vdw 2.291 3.040 nonbonded pdb=" OE1 GLU B 12 " pdb=" N GLY B 125 " model vdw 2.347 3.120 nonbonded pdb=" O CYS B 28 " pdb=" OG1 THR B 84 " model vdw 2.357 3.040 ... (remaining 27481 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.400 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 3719 Z= 0.205 Angle : 0.733 16.060 5054 Z= 0.340 Chirality : 0.037 0.166 572 Planarity : 0.004 0.059 604 Dihedral : 16.470 152.308 1297 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.40), residues: 436 helix: 0.55 (0.32), residues: 249 sheet: 0.04 (0.84), residues: 44 loop : -1.00 (0.54), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.001 0.000 HIS A 101 PHE 0.016 0.001 PHE A 275 TYR 0.017 0.001 TYR A 92 ARG 0.007 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.27497 ( 231) hydrogen bonds : angle 8.01179 ( 678) SS BOND : bond 0.00141 ( 1) SS BOND : angle 0.38125 ( 2) covalent geometry : bond 0.00417 ( 3718) covalent geometry : angle 0.73320 ( 5052) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.508 Fit side-chains REVERT: A 146 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8783 (tm-30) REVERT: A 279 LYS cc_start: 0.7234 (tttt) cc_final: 0.6998 (mttt) REVERT: B 42 TRP cc_start: 0.8513 (m100) cc_final: 0.7949 (m100) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1904 time to fit residues: 30.0299 Evaluate side-chains 114 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.4980 chunk 32 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN A 277 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.167053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.139688 restraints weight = 5190.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138586 restraints weight = 7818.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.139000 restraints weight = 7512.536| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3719 Z= 0.153 Angle : 0.596 6.635 5054 Z= 0.308 Chirality : 0.041 0.137 572 Planarity : 0.004 0.052 604 Dihedral : 10.769 107.682 524 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.26 % Allowed : 5.67 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.40), residues: 436 helix: 1.11 (0.30), residues: 262 sheet: 0.50 (0.78), residues: 50 loop : -1.00 (0.61), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 177 HIS 0.001 0.000 HIS A 250 PHE 0.023 0.001 PHE A 225 TYR 0.018 0.001 TYR A 208 ARG 0.006 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04540 ( 231) hydrogen bonds : angle 4.59347 ( 678) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.15540 ( 2) covalent geometry : bond 0.00336 ( 3718) covalent geometry : angle 0.59647 ( 5052) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.379 Fit side-chains REVERT: A 259 MET cc_start: 0.8138 (mmp) cc_final: 0.7702 (mmp) REVERT: B 37 ILE cc_start: 0.9197 (mm) cc_final: 0.8724 (mt) outliers start: 1 outliers final: 0 residues processed: 140 average time/residue: 0.1514 time to fit residues: 26.1073 Evaluate side-chains 116 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 25 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.168618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.140513 restraints weight = 5230.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139041 restraints weight = 9519.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140171 restraints weight = 8621.926| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3719 Z= 0.149 Angle : 0.590 7.495 5054 Z= 0.300 Chirality : 0.040 0.142 572 Planarity : 0.004 0.050 604 Dihedral : 9.230 75.593 524 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.26 % Allowed : 4.90 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.40), residues: 436 helix: 1.23 (0.30), residues: 262 sheet: 0.24 (0.76), residues: 48 loop : -1.22 (0.59), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 177 HIS 0.001 0.000 HIS A 250 PHE 0.016 0.001 PHE A 47 TYR 0.035 0.002 TYR B 39 ARG 0.009 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 231) hydrogen bonds : angle 4.32010 ( 678) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.12647 ( 2) covalent geometry : bond 0.00334 ( 3718) covalent geometry : angle 0.58981 ( 5052) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.387 Fit side-chains REVERT: A 137 PHE cc_start: 0.7667 (m-10) cc_final: 0.7458 (m-10) REVERT: A 202 LYS cc_start: 0.8508 (mttt) cc_final: 0.8252 (mttt) REVERT: B 52 GLU cc_start: 0.7639 (pm20) cc_final: 0.7409 (pm20) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.1631 time to fit residues: 27.8235 Evaluate side-chains 123 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.0980 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.166529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.137940 restraints weight = 5072.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.136543 restraints weight = 7566.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137141 restraints weight = 7645.962| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3719 Z= 0.131 Angle : 0.588 7.344 5054 Z= 0.294 Chirality : 0.039 0.128 572 Planarity : 0.004 0.054 604 Dihedral : 8.341 61.948 524 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.40), residues: 436 helix: 1.28 (0.30), residues: 264 sheet: 0.04 (0.73), residues: 50 loop : -1.25 (0.61), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 177 HIS 0.002 0.001 HIS A 250 PHE 0.014 0.001 PHE A 225 TYR 0.018 0.001 TYR B 39 ARG 0.003 0.000 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03607 ( 231) hydrogen bonds : angle 4.02677 ( 678) SS BOND : bond 0.00830 ( 1) SS BOND : angle 0.20840 ( 2) covalent geometry : bond 0.00292 ( 3718) covalent geometry : angle 0.58801 ( 5052) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 91 ARG cc_start: 0.7081 (ttm110) cc_final: 0.6861 (ttm110) REVERT: A 140 TYR cc_start: 0.9322 (m-80) cc_final: 0.9047 (m-10) REVERT: B 39 TYR cc_start: 0.8908 (m-80) cc_final: 0.8605 (m-80) REVERT: B 52 GLU cc_start: 0.7694 (pm20) cc_final: 0.7444 (pm20) REVERT: B 107 ASN cc_start: 0.8133 (t0) cc_final: 0.7868 (t0) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1925 time to fit residues: 34.4997 Evaluate side-chains 126 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 1 optimal weight: 0.0670 chunk 22 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.165390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135649 restraints weight = 5287.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134401 restraints weight = 5282.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.133924 restraints weight = 5473.122| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3719 Z= 0.146 Angle : 0.619 7.444 5054 Z= 0.306 Chirality : 0.040 0.135 572 Planarity : 0.004 0.055 604 Dihedral : 8.218 62.962 524 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.40), residues: 436 helix: 1.30 (0.30), residues: 264 sheet: 0.01 (0.71), residues: 50 loop : -1.14 (0.62), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.002 0.001 HIS A 56 PHE 0.011 0.001 PHE A 225 TYR 0.018 0.001 TYR A 92 ARG 0.003 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03671 ( 231) hydrogen bonds : angle 4.00947 ( 678) SS BOND : bond 0.00280 ( 1) SS BOND : angle 0.32444 ( 2) covalent geometry : bond 0.00328 ( 3718) covalent geometry : angle 0.61948 ( 5052) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.465 Fit side-chains REVERT: A 202 LYS cc_start: 0.8559 (mttt) cc_final: 0.8355 (mttt) REVERT: B 101 TYR cc_start: 0.8390 (m-10) cc_final: 0.8087 (m-10) REVERT: B 107 ASN cc_start: 0.8214 (t0) cc_final: 0.7954 (t0) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1875 time to fit residues: 32.2699 Evaluate side-chains 119 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 10 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 21 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 28 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.167689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.139024 restraints weight = 5324.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.137431 restraints weight = 7169.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.138480 restraints weight = 7560.367| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3719 Z= 0.146 Angle : 0.622 7.439 5054 Z= 0.307 Chirality : 0.040 0.136 572 Planarity : 0.004 0.055 604 Dihedral : 8.197 63.844 524 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.41), residues: 436 helix: 1.36 (0.30), residues: 264 sheet: 0.40 (0.87), residues: 39 loop : -0.95 (0.60), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 56 PHE 0.010 0.001 PHE A 225 TYR 0.020 0.002 TYR A 92 ARG 0.004 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 231) hydrogen bonds : angle 3.92686 ( 678) SS BOND : bond 0.00093 ( 1) SS BOND : angle 0.30044 ( 2) covalent geometry : bond 0.00333 ( 3718) covalent geometry : angle 0.62201 ( 5052) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 0.432 Fit side-chains REVERT: B 107 ASN cc_start: 0.8229 (t0) cc_final: 0.7974 (t0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.1980 time to fit residues: 33.2002 Evaluate side-chains 115 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 20 optimal weight: 0.3980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS A 121 HIS A 150 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.165516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.137215 restraints weight = 5236.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.135178 restraints weight = 8186.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.135481 restraints weight = 8156.824| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3719 Z= 0.133 Angle : 0.631 7.449 5054 Z= 0.312 Chirality : 0.040 0.130 572 Planarity : 0.004 0.057 604 Dihedral : 8.101 61.978 524 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.40), residues: 436 helix: 1.17 (0.30), residues: 266 sheet: 0.13 (0.73), residues: 50 loop : -1.13 (0.64), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 62 HIS 0.003 0.001 HIS A 101 PHE 0.028 0.001 PHE A 47 TYR 0.031 0.002 TYR A 92 ARG 0.003 0.001 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03488 ( 231) hydrogen bonds : angle 4.02002 ( 678) SS BOND : bond 0.00140 ( 1) SS BOND : angle 0.16274 ( 2) covalent geometry : bond 0.00297 ( 3718) covalent geometry : angle 0.63115 ( 5052) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.493 Fit side-chains REVERT: A 187 ARG cc_start: 0.6594 (ttt180) cc_final: 0.6177 (ttp-170) REVERT: A 260 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 264 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7586 (mtt90) REVERT: B 42 TRP cc_start: 0.8633 (m100) cc_final: 0.7917 (m100) REVERT: B 107 ASN cc_start: 0.8292 (t0) cc_final: 0.8072 (t0) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1882 time to fit residues: 30.9192 Evaluate side-chains 113 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.0980 chunk 29 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS B 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138211 restraints weight = 5177.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.137162 restraints weight = 5295.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.137101 restraints weight = 5493.012| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3719 Z= 0.125 Angle : 0.628 7.358 5054 Z= 0.307 Chirality : 0.040 0.185 572 Planarity : 0.004 0.059 604 Dihedral : 7.910 59.617 524 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.26 % Allowed : 1.55 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.40), residues: 436 helix: 1.32 (0.30), residues: 264 sheet: 0.11 (0.72), residues: 50 loop : -1.11 (0.63), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 177 HIS 0.002 0.001 HIS A 101 PHE 0.024 0.001 PHE A 47 TYR 0.032 0.001 TYR A 92 ARG 0.003 0.001 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.03336 ( 231) hydrogen bonds : angle 3.94007 ( 678) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.44593 ( 2) covalent geometry : bond 0.00279 ( 3718) covalent geometry : angle 0.62830 ( 5052) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 0.504 Fit side-chains REVERT: A 343 TYR cc_start: 0.7169 (m-80) cc_final: 0.6906 (m-80) REVERT: B 26 LEU cc_start: 0.7084 (mp) cc_final: 0.6621 (mp) REVERT: B 42 TRP cc_start: 0.8601 (m100) cc_final: 0.7960 (m100) outliers start: 1 outliers final: 0 residues processed: 132 average time/residue: 0.2232 time to fit residues: 36.3780 Evaluate side-chains 109 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 12 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS A 183 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.167075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.140710 restraints weight = 5106.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.139303 restraints weight = 7812.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.139490 restraints weight = 8232.107| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3719 Z= 0.141 Angle : 0.652 7.913 5054 Z= 0.320 Chirality : 0.041 0.173 572 Planarity : 0.004 0.058 604 Dihedral : 7.987 59.654 524 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.41), residues: 436 helix: 1.29 (0.30), residues: 265 sheet: 0.42 (0.88), residues: 39 loop : -1.05 (0.60), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 93 HIS 0.002 0.000 HIS A 101 PHE 0.023 0.001 PHE A 47 TYR 0.024 0.001 TYR B 38 ARG 0.008 0.001 ARG A 264 Details of bonding type rmsd hydrogen bonds : bond 0.03534 ( 231) hydrogen bonds : angle 3.93866 ( 678) SS BOND : bond 0.00072 ( 1) SS BOND : angle 0.65272 ( 2) covalent geometry : bond 0.00321 ( 3718) covalent geometry : angle 0.65205 ( 5052) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.327 Fit side-chains REVERT: A 202 LYS cc_start: 0.8529 (mttt) cc_final: 0.8153 (mttm) REVERT: A 217 MET cc_start: 0.8214 (mmp) cc_final: 0.7896 (tpp) REVERT: A 343 TYR cc_start: 0.7216 (m-80) cc_final: 0.6924 (m-80) REVERT: B 26 LEU cc_start: 0.7022 (mp) cc_final: 0.6465 (mp) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1499 time to fit residues: 23.4529 Evaluate side-chains 107 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 18 optimal weight: 0.0170 chunk 17 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.169372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.141088 restraints weight = 5362.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.139787 restraints weight = 8775.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.139287 restraints weight = 8943.529| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3719 Z= 0.135 Angle : 0.666 8.563 5054 Z= 0.327 Chirality : 0.041 0.129 572 Planarity : 0.005 0.059 604 Dihedral : 7.972 57.385 524 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.41), residues: 436 helix: 1.27 (0.30), residues: 266 sheet: 0.56 (0.76), residues: 52 loop : -1.04 (0.65), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 122 HIS 0.001 0.000 HIS A 101 PHE 0.022 0.001 PHE A 47 TYR 0.026 0.001 TYR A 92 ARG 0.007 0.001 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 231) hydrogen bonds : angle 3.89950 ( 678) SS BOND : bond 0.00107 ( 1) SS BOND : angle 0.22156 ( 2) covalent geometry : bond 0.00300 ( 3718) covalent geometry : angle 0.66575 ( 5052) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 872 Ramachandran restraints generated. 436 Oldfield, 0 Emsley, 436 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 343 TYR cc_start: 0.7143 (m-80) cc_final: 0.6925 (m-80) REVERT: B 26 LEU cc_start: 0.7240 (mp) cc_final: 0.6674 (mp) REVERT: B 42 TRP cc_start: 0.8666 (m100) cc_final: 0.8026 (m100) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.2337 time to fit residues: 36.7004 Evaluate side-chains 109 residues out of total 388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 109 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.0040 chunk 33 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.167588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137958 restraints weight = 5252.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137875 restraints weight = 5330.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.137875 restraints weight = 5480.558| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3719 Z= 0.142 Angle : 0.685 8.549 5054 Z= 0.334 Chirality : 0.041 0.124 572 Planarity : 0.004 0.058 604 Dihedral : 8.079 56.630 524 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.41), residues: 436 helix: 1.21 (0.30), residues: 267 sheet: 0.81 (0.85), residues: 38 loop : -1.14 (0.60), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 122 HIS 0.001 0.000 HIS A 56 PHE 0.022 0.001 PHE A 47 TYR 0.016 0.001 TYR A 291 ARG 0.008 0.001 ARG A 91 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 231) hydrogen bonds : angle 3.90035 ( 678) SS BOND : bond 0.00192 ( 1) SS BOND : angle 0.46361 ( 2) covalent geometry : bond 0.00325 ( 3718) covalent geometry : angle 0.68534 ( 5052) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2011.37 seconds wall clock time: 37 minutes 48.67 seconds (2268.67 seconds total)